Threshold Filtering

Threshold filters, following the guidance of Florida Department of Environmental Protection’s (FDEP) Division of Environmental Assessment and Restoration (DEAR) are used to exclude specific results values from the SEACAR Analysis. Based on the threshold filters, Quality Assurance / Quality Control (QAQC) Flags are inserted into the SEACAR_QAQCFlagCode and SEACAR_QAQC_Description columns of the export data. The Include column indicates whether the QAQC Flag will also indicate that data are excluded from analysis. No data are excluded from the data export, but the analysis scripts can use the Include column to exclude data (1 to include, 0 to exclude).

Continuous Water Quality threshold values
Parameter Name Units Low Threshold High Threshold Sensor Type
Dissolved Oxygen mg/L 0 50 YSI EXOs
Dissolved Oxygen mg/L 0 50 Analysis Only - 2022-04-04
Dissolved Oxygen mg/L 0 50 6600 Series
Salinity ppt 0 70 6600 Series
Salinity ppt 0 70 YSI EXOs
Salinity ppt 0 70 Analysis Only - 2022-04-04
Water Temperature Degrees C -5 45 YSI EXOs
Water Temperature Degrees C -5 45 Analysis Only - 2022-04-04
Water Temperature Degrees C -5 45 6600 Series
pH pH 2 14 Analysis Only - 2022-04-04
pH pH 2 14 6600 Series
pH pH 2 14 YSI EXOs
Dissolved Oxygen Saturation % 0 500 YSI EXOs
Dissolved Oxygen Saturation % 0 500 6600 Series
Dissolved Oxygen Saturation % 0 500 Analysis Only - 2022-04-04
Specific Conductivity mS/cm 0 100 6600 Series
Specific Conductivity mS/cm 0 200 YSI EXOs
Turbidity NTU 0 4000 YSI EXOs
Turbidity NTU 0 1000 6600 Series
Turbidity NTU 0 4000 Analysis Only - 2022-04-04
Discrete Water Quality threshold values
Parameter Name Units Low Threshold High Threshold
Dissolved Oxygen mg/L 0.000001 22
Salinity ppt 0 70
Water Temperature Degrees C 3 40
pH 2 13
Dissolved Oxygen Saturation % 0.000001 310
Specific Conductivity mS/cm 0.005000001 100
Turbidity NTU 0 -
Total Suspended Solids (TSS) mg/L 0 -
Chlorophyll a uncorrected for pheophytin ug/L 0 -
Chlorophyll a corrected for pheophytin ug/L 0 -
Secchi Depth m 0.000001 50
Light Extinction Coefficient m^1 0 -
Colored dissolved organic matter, CDOM PCU 0 -
Fluorescent dissolved organic matter, FDOM QSE 0 -
Total Nitrogen mg/L 0 -
Total Kjeldahl Nitrogen TKN mg/L 0 -
NO2+3 Filtered mg/L 0 -
NH4 Filtered mg/L 0 -
Total Phosphorus mg/L 0 -
PO4 Filtered mg/L 0 -
Ammonia- Un-ionized (NH3) mg/L 0 -
Nitrate (N) mg/L 0 -
Nitrite (N) mg/L 0 -
Nitrogen, organic mg/L 0 -
Quality Assurance Flags inserted based on threshold checks listed in Table 1 & 2
SEACAR QAQC Description Include SEACAR QAQCFlagCode
Exceeds Maximum threshold. Not verified in raw data No 2Q
Exceeds Maximum threshold. Verified in raw data No 3Q
Below Minimum threshold. Not verified in raw data No 4Q
Below Minimum threshold. Verified in raw data No 5Q
Within threshold tolerance Yes 6Q
No defined thresholds for this parameter Yes 7Q

Value Qualifiers

Value qualifier codes included within the data are used to exclude certain results from the analysis. The data are retained in the data export files, but the analysis uses the Include column to filter the results.

STORET and WIN value qualifier codes

Value qualifier codes from STORET and WIN data are examined with the database and used to populate the Include column in data exports.

Value Qualifier codes excluded from analysis
Qualifier Source Value Qualifier Include MDL Description
STORET-WIN H No 0 Value based on field kit determination; results may not be accurate
STORET-WIN J No 0 Estimated value
STORET-WIN V No 0 Analyte was detected at or above method detection limit
STORET-WIN Y No 0

Discrete Water Quality Value Qualifiers

The following value qualifiers are highlighted in the Discrete Water Quality section of this report. An exception is made for Program 476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network and data flagged with Value Qualifier H are included for this program only.

H - Value based on field kit determiniation; results may not be accurate. This code shall be used if a field screening test (e.g., field gas chromatograph data, immunoassay, or vendor-supplied field kit) was used to generate the value and the field kit or method has not been recognized by the Department as equivalent to laboratory methods.

I - The reported value is greater than or equal to the laboratory method detection limit but less than the laboratory practical quantitation limit.

Q - Sample held beyond the accepted holding time. This code shall be used if the value is derived from a sample that was prepared or analyzed after the approved holding time restrictions for sample preparation or analysis.

S - Secchi disk visible to bottom of waterbody. The value reported is the depth of the waterbody at the location of the Secchi disk measurement.

U - Indicates that the compound was analyzed for but not detected. This symbol shall be used to indicate that the specified component was not detected. The value associated with the qualifier shall be the laboratory method detection limit. Unless requested by the client, less than the method detection limit values shall not be reported

Systemwide Monitoring Program (SWMP) value qualifier codes

Value qualifier codes from the SWMP continuous program are examined with the database and used to populate the Include column in data exports. SWMP Qualifier Codes are indicated by QualifierSource=SWMP.

SWMP Value Qualifier codes
Qualifier Source Value Qualifier Include Description
SWMP -1 Yes Optional parameter not collected
SWMP -2 No Missing data
SWMP -3 No Data rejected due to QA/QC
SWMP -4 No Outside low sensor range
SWMP -5 No Outside high sensor range
SWMP 0 Yes Passed initial QA/QC checks
SWMP 1 No Suspect data
SWMP 2 Yes Reserved for future use
SWMP 3 Yes
SWMP 4 Yes Historical: Pre-auto QA/QC
SWMP 5 Yes Corrected data

Water Column

The water column habitat extends from the surface of all water bodies to the bottom sediments and encompasses the different features found in the water at different depths (National Oceanographic Center, 2016). The water column habitat must be viewed in relation to its interconnectedness with other habitats. A healthy water column is an integral component in ensuring a healthy marine and coastal ecosystem. Having a flourishing marine and coastal ecosystem in Florida is necessary to support a strong economy. The health of the water column is dependent upon factors as diverse as land use (e.g., agriculture, mining, forestry practices); human population growth; emissions, (e.g., power plants, automobiles, wastewater); climate (e.g., rainfall, temperature, winds and currents); and decadal trends (e.g., El Niño/La Niña, Atlantic Multidecadal Oscillation, climate change).

The water column is composed of various physical, chemical and biological features, and only a small number of them are adequately monitored. Features of the water column that are monitored are used as indicators of the water column health and help assess the status of other habitats. These indicators include nutrient concentrations (nitrogen and phosphorus); water quality (dissolved oxygen, temperature, salinity and pH); water clarity (Secchi depth, turbidity, chlorophyll-a and colored dissolved organic matter); and nekton (fish, macroinvertebrates and megafauna).

Seasonal Kendall-Tau Analysis

Indicators must have a minimum of five to ten years, depending on the habitat, of data within the geographic range of the analysis to be included in the analysis. Ten years of data are required for discrete parameters, and five years of data are required for continuous parameters. If there are insufficient years of data, the number of years of data available will be noted and labeled as “insufficient data to conduct analysis”. Further, for the preferred Seasonal Kendall-Tau test, there must be data from at least two months in common across at least two consecutive years within the RCP managed area being analyzed. Values that pass both of these tests will be included in the analysis and be labeled as Use_In_Analysis = TRUE. Any that fail either test will be excluded from the analyses and labeled as Use_In_Analysis = FALSE.

Water Quality - Discrete

The following files were used in the discrete analysis:

  • Combined_WQ_WC_NUT_Chlorophyll_a_corrected_for_pheophytin-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_Chlorophyll_a_uncorrected_for_pheophytin-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_Colored_dissolved_organic_matter_CDOM-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_Dissolved_Oxygen-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_Dissolved_Oxygen_Saturation-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_pH-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_Salinity-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_Secchi_Depth-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_Total_Nitrogen-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_Total_Phosphorus-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_Total_Suspended_Solids_TSS-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_Turbidity-2024-Feb-22.txt

  • Combined_WQ_WC_NUT_Water_Temperature-2024-Feb-22.txt

Dissolved Oxygen - Discrete Water Quality

Dissolved Oxygen (DO) is a key indicator of water quality. Oxygen enters surface waters by air-sea gas exchange, by wind action, or as a byproduct of aquatic plant photosynthesis. The actual quantity of DO in aquatic environments is dependent on the above processes as well as water temperature and salinity.

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for Dissolved Oxygen
Discrete Water Quality
The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for Dissolved Oxygen
ProgramID N_Data YearMin YearMax
69 1203 2001 2017
5002 70 2000 2023
103 56 2004 2021
95 47 2014 2018
115 2 1994 1994

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program
5002 - Florida STORET / WIN
103 - EPA STOrage and RETrieval Data Warehouse (STORET)
95 - Harmful Algal Bloom Marine Observation Network
115 - Environmental Monitoring Assessment Program

There are no qualifying Value Qualifiers for Dissolved Oxygen in Fort Clinch State Park Aquatic Preserve

pH - Discrete Water Quality

The pH of water is the measure of how acidic or basic the water body is on a scale of 0-14, with lower readings indicating acidic and higher readings indicating basic, and a pH of 7 being neutral. Florida’s natural waters fall between 6.5 and 8.5 on this scale. A water body’s pH can change due to precipitation, geology, vegetation, water pollution and air pollution.

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for pH
Discrete Water Quality
The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for pH
ProgramID N_Data YearMin YearMax
69 1215 2001 2017
5002 72 2000 2023
95 48 2014 2018
103 45 2004 2021
115 1 1994 1994

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program
5002 - Florida STORET / WIN
95 - Harmful Algal Bloom Marine Observation Network
103 - EPA STOrage and RETrieval Data Warehouse (STORET)
115 - Environmental Monitoring Assessment Program

There are no qualifying Value Qualifiers for pH in Fort Clinch State Park Aquatic Preserve

Salinity - Discrete Water Quality

Salinity is a measure of the amount of salt in the water. In estuarine ecosystems, salinity is influenced by precipitation, evaporation, surface-water inputs, and exchange with coastal waters.

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for Salinity
Discrete Water Quality
The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for Salinity
ProgramID N_Data YearMin YearMax
69 1218 2001 2017
5002 67 2000 2022
95 52 1999 2018
103 43 2004 2007
115 2 1994 1994

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program
5002 - Florida STORET / WIN
95 - Harmful Algal Bloom Marine Observation Network
103 - EPA STOrage and RETrieval Data Warehouse (STORET)
115 - Environmental Monitoring Assessment Program

There are no qualifying Value Qualifiers for Salinity in Fort Clinch State Park Aquatic Preserve

Secchi Depth - Discrete Water Quality

Secchi depth is a measure of the transparency or clarity of the water by a device called a Secchi disk. A Secchi disk is a black and white disk that is lowered into the water on a cord. The Secchi depth is the depth at which the disk can no longer be seen. The deeper the Secchi depth, the greater the water clarity.

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for Secchi Depth
Discrete Water Quality
The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for Secchi Depth
ProgramID N_Data YearMin YearMax
69 1209 2001 2017
5002 34 2000 2014
103 2 2007 2007

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program
5002 - Florida STORET / WIN
103 - EPA STOrage and RETrieval Data Warehouse (STORET)

There are no qualifying Value Qualifiers for Secchi Depth in Fort Clinch State Park Aquatic Preserve

Total Nitrogen - Discrete Water Quality

Nitrogen and Phosphorous are key nutrients that provide nourishment essential for the growth and maintenance of aquatic plants and animals; however, excess nutrients can cause harmful algal blooms and other water quality concerns. Nutrients enter water bodies several ways, including runoff from rain events and atmospheric deposition from natural and industrial sources.

Total Nitrogen Calculation:

The logic for calculated Total Nitrogen was provided by Kevin O’Donnell and colleagues at FDEP (with the help of Jay Silvanima, Watershed Monitoring Section). The following logic is used, in this order, based on the availability of specific nitrogen components.

  1. TN = TKN + NO3O2;
  2. TN = TKN + NO3 + NO2;
  3. TN = ORGN + NH4 + NO3O2;
  4. TN = ORGN + NH4 + NO2 + NO3;
  5. TN = TKN + NO3;
  6. TN = ORGN + NH4 + NO3;

Additional Information:

  • Rules for use of sample fraction:
    • FDEP report that if both “Total” and “Dissolved” are reported, only “Total” is used. If the total is not reported, they do use dissolved as a best available replacement.
    • An analysis of all SEACAR data shows that 90% of all possible TN calculations can be done using nitrogen components with the same sample fraction, rather than use nitrogen components with mixed total/dissolved sample fractions. In other words, TN can be calculated when TKN and NO3O2 are both total sample fraction, or when both are dissolved sample fraction. This is important, because then the calculated TN value is not based on components with mixed sample fractions.
  • Values inserted into data:
    • ParameterName = “Total Nitrogen”
    • SEACAR_QAQCFlagCode = “1Q”
    • SEACAR_QAQC_Description = “SEACAR Calculated”
      Seasonal Kendall-Tau Trend Analysis
      Discrete Water Quality
      Map showing location of Discrete sampling sites for Total Nitrogen
      Discrete Water Quality
      The bubble size on the above plots reflects the amount of data available at each sampling site
Programs contributing data for Total Nitrogen
ProgramID N_Data YearMin YearMax
5002 43 2000 2023
103 9 2004 2006

Program names:

5002 - Florida STORET / WIN
103 - EPA STOrage and RETrieval Data Warehouse (STORET)

There are no qualifying Value Qualifiers for Total Nitrogen in Fort Clinch State Park Aquatic Preserve

Total Phosphorus - Discrete Water Quality

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for Total Phosphorus
Discrete Water Quality
The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for Total Phosphorus
ProgramID N_Data YearMin YearMax
5002 47 2000 2023
103 10 2004 2021

Program names:

5002 - Florida STORET / WIN
103 - EPA STOrage and RETrieval Data Warehouse (STORET)

There are no qualifying Value Qualifiers for Total Phosphorus in Fort Clinch State Park Aquatic Preserve

Water Temperature - Discrete Water Quality

Temperature determines the capacity of water to hold oxygen. Cooler water can hold more dissolved oxygen because water molecules are more tightly packed, making it harder for oxygen to escape. Additionally, as water temperature increases, fish and other aquatic organisms become more active and consume oxygen at a faster rate.

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for Water Temperature
Discrete Water Quality
The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for Water Temperature
ProgramID N_Data YearMin YearMax
69 1219 2001 2017
5002 72 2000 2023
103 55 2004 2021
95 51 2014 2018
115 2 1994 1994

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program
5002 - Florida STORET / WIN
103 - EPA STOrage and RETrieval Data Warehouse (STORET)
95 - Harmful Algal Bloom Marine Observation Network
115 - Environmental Monitoring Assessment Program

There are no qualifying Value Qualifiers for Water Temperature in Fort Clinch State Park Aquatic Preserve